From 7a3a9a571db17f70f6cc0d6bec6661207ca491e7 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 25 Sep 2024 18:00:13 +0000 Subject: [PATCH 1/2] adding rasusa version 2.1.0 --- README.md | 2 +- rasusa/2.1.0/Dockerfile | 54 +++++++++++++++++++++++++++++++++++++++++ rasusa/2.1.0/README.md | 32 ++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 1 deletion(-) create mode 100644 rasusa/2.1.0/Dockerfile create mode 100644 rasusa/2.1.0/README.md diff --git a/README.md b/README.md index bda448883..7317c8cfb 100644 --- a/README.md +++ b/README.md @@ -252,7 +252,7 @@ To learn more about the docker pull rate limits and the open source software pro | [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| |
  • https://github.com/lbcb-sci/racon
  • https://github.com/isovic/racon (ARCHIVED)
    • | -| [rasusa](https://hub.docker.com/r/staphb/rasusa/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | +| [rasusa](https://hub.docker.com/r/staphb/rasusa/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | | [raven](https://hub.docker.com/r/staphb/raven/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | | https://github.com/lbcb-sci/raven | | [RAxML](https://hub.docker.com/r/staphb/raxml/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | | https://github.com/stamatak/standard-RAxML | | [RAxML-NG](https://hub.docker.com/r/staphb/raxml-ng/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml-ng)](https://hub.docker.com/r/staphb/raxml-ng) | | https://github.com/amkozlov/raxml-ng | diff --git a/rasusa/2.1.0/Dockerfile b/rasusa/2.1.0/Dockerfile new file mode 100644 index 000000000..66e6ab4f3 --- /dev/null +++ b/rasusa/2.1.0/Dockerfile @@ -0,0 +1,54 @@ +FROM ubuntu:jammy as app + +ARG RASUSA_VER="2.1.0" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="rasusa" +LABEL software.version="${RASUSA_VER}" +LABEL description="Randomly subsample sequencing reads to a specified coverage." +LABEL website="https://github.com/mbhall88/rasusa" +LABEL license="https://github.com/mbhall88/rasusa/blob/master/LICENSE" +LABEL maintainer="Jake Garfin" +LABEL maintainer.email="jake.garfin@state.mn.us" +LABEL maintainer2="Curtis Kapsak" +LABEL maintainer2.email="kapsakcj@gmail.com" +LABEL maintainer3="Erin Young" +LABEL maintainer3.email="eriny@utah.gov" + +# install wget and cleanup apt garbage +RUN apt-get update && apt-get -y install --no-install-recommends \ + wget \ + ca-certificates \ + procps && \ + apt-get autoclean && \ + rm -rf /var/lib/apt/lists/* + +# install rasusa +RUN wget -q https://github.com/mbhall88/rasusa/releases/download/${RASUSA_VER}/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ + tar -xvf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ + rm -rf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ + mkdir /data + +# set PATH and perl locale settings +ENV PATH="${PATH}:/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl/" \ + LC_ALL=C + +WORKDIR /data + +CMD rasusa --help + +FROM app as test + +# print version and help options +RUN rasusa --version && rasusa --help + +# cannot run rust-based test, since rust isn't installed, but just testing basic command on SC2 reads in our repo +# inputs FASTQs each have 80867 reads +# output FASTQs should have 40434 reads in each (about 1/2 of input) +# -s 1 is for setting a specific seed +# -O is for gzip compression on output FASTQs +RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ + wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \ + rasusa reads --num 40434 -s 1 -O g -o SRR13957123_downsampled_1.fastq.gz -o SRR13957123_downsampled_2.fastq.gz SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz && \ + ls -lh diff --git a/rasusa/2.1.0/README.md b/rasusa/2.1.0/README.md new file mode 100644 index 000000000..ffa71ab15 --- /dev/null +++ b/rasusa/2.1.0/README.md @@ -0,0 +1,32 @@ +# Rasusa container + +Main tool : [Rasusa](https://github.com/mbhall88/rasusa) + +Additional tools: + +- none + +Full documentation: https://github.com/mbhall88/rasusa + +Randomly subsample sequencing reads to a specified coverage + +## Example Usage + +```bash +# sars-cov-2 example, paired-end illumina +rasusa reads \ + -n 40434 \ # downsample to specific number of reads per FASTQ file + -s 1 \ # set seed + -O g \ # set output file compression format as gzip + -o SRR13957123_downsampled_1.fastq.gz -o SRR13957123_downsampled_2.fastq.gz \ + SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz + +# Salmonella enterica example, paired-end illumina +rasusa reads \ + --coverage 100 \ # use 100X coverage for downsampling + --genome-size 5M \ # downsample to specific coverage based on genome size (5 million bases) + -s 1 \ # set seed + -O g \ # set output file compression format as gzip + -o SRR10992628_downsampled_1.fastq.gz -o SRR10992628_downsampled_2.fastq.gz \ + SRR10992628_1.fastq.gz SRR10992628_2.fastq.gz +``` From ca9de96bc9c26ba5379f45ec4d5d3c77c60f895c Mon Sep 17 00:00:00 2001 From: Erin Young Date: Tue, 29 Oct 2024 17:58:33 +0000 Subject: [PATCH 2/2] gnu --- rasusa/2.1.0/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/rasusa/2.1.0/Dockerfile b/rasusa/2.1.0/Dockerfile index 66e6ab4f3..7c8b0ce7c 100644 --- a/rasusa/2.1.0/Dockerfile +++ b/rasusa/2.1.0/Dockerfile @@ -25,13 +25,13 @@ RUN apt-get update && apt-get -y install --no-install-recommends \ rm -rf /var/lib/apt/lists/* # install rasusa -RUN wget -q https://github.com/mbhall88/rasusa/releases/download/${RASUSA_VER}/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ - tar -xvf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ - rm -rf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ +RUN wget -q https://github.com/mbhall88/rasusa/releases/download/${RASUSA_VER}/rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \ + tar -xvf rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \ + rm -rf rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \ mkdir /data # set PATH and perl locale settings -ENV PATH="${PATH}:/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl/" \ +ENV PATH="${PATH}:/rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu/" \ LC_ALL=C WORKDIR /data